Historical novels are a genre, like mysteries and science fiction. They do have some presumptions. Books like War and Peace and Middlemarch are historical novels, deliberately set in an earlier era. But the differences between these two books are instructive in thinking about the vastly larger genre we have in our era.
W&P deals explicitly with the big events of the day: the invasion of Russia, the defeat of Napoleon. And it has big shot historical figures as actual characters, like Napoleon himself, General Kutuzov, etc. Middlemarch is set in an era with specific social and economic relations, but (as far as I know), deals entirely with invented characters, dealing with intimate personal issues--more properly large social issues as expressed through personal situations.
And, as I suppose must be mentioned, W&P was written by a man, Middlemarch by a woman, though I didn't consciously think of that when I picked them. Boy's historical novels (battles, kings), girl's historical novels (loveless marriages, frustrated ambitions).
In this taxonomy The Thousand Autumns of Jacob de Zoet is clearly a boy's historical novel: trade, battles, kidnappings, sinister monasteries. I enjoyed it a great deal.
But, while I was reading it, I felt I was reading a Neal Stephenson novel. It had all those Stephenson features: detailed explications of proto-modern phenomena like bookkeeping, mysteriously well-organized cults with ridiculous obsessions, plucky underarmed heroes defeating well-armed forces through pluck and guile. I love Stephenson (aside from that great Long-Now clock weight of a book, Anathem), but had never thought of him having influence on other writers. He seems too idiosyncratic for that.
Stephenson-style historical novels involve a bunch of people in the past trying desperately to figure out how to be us. They mirror our obsessions and our interests within the physical constraints of their environments.
In that sense, Jacob de Zoet is not entirely a Stephenson novel. Many of the characters do, in fact, think about their world the way someone who actually lived in it would.
But the most Stephenson-like aspect of the novel is that weird monastery cult. Mitchell spends an inordinate amount of time on this science-fictional organization. Like all Stephenson cults, both good and evil, it is well-organized, secretive, and obsessed. In this case, it has an organization of captives, and one of captors. No need to go into any more detail than that. It involves elaborate plots, meetings, rugged geographies, betrayals, and illusions within illusions.
All of it is great fun. I lack the faith in organization (or the mental organization, for that matter) to write a Stephenson novel, but I sure do enjoy reading them.